Publications

Interoceptive technologies for psychiatric interventions: From diagnosis to clinical applications
Felix Schoeller
Adam Haar Horowitz
Abhinandan Jain
Pattie Maes
Nicco Reggente
Leonardo Christov-Moore
Giovanni Pezzulo
Laura Barca
Micah Allen
Roy Salomon
Mark Miller
Daniele Di Lernia
Giuseppe Riva
Manos Tsakiris
Moussa A. Chalah
Arno Klein
Ben Zhang
Teresa Garcia
Ursula Pollack
Marion Trousselard … (see 4 more)
Charles Verdonk
Vladimir Adrien
Karl Friston

The perception of body signals play a crucial role in cognition and emotion, which may lead to catastrophic outcomes when it becomes dysf… (see more)unctional. To characterize these mechanisms and intervene on interoception for either diagnostic or treatment purposes, a mounting body of research is concerned with interventions on interoceptive channels such as respiration, cardioception, or thermoception. However, we are still lacking a mechanistic understanding of the underlying psychophysiology. For example, interoceptive signals are often both the cause and consequences of some distress in various mental disorders, and it is still unclear how interoceptive signals bind with exteroceptive cues. In this article, we present existing technologies for manipulating interoception and review their clinical potential in light of the predictive processing framework describing interoception as a process of minimization of prediction errors. We distinguish between three kinds of stimuli: artificial sensations that concern the direct manipulation of interoceptive signals, interoceptive illusions that manipulate contextual cues to induce a predictable drift in body perception, and emotional augmentation technologies that blend artificial sensations with contextual cues of personal significance to generate specific moods or emotions. We discuss how each technology can assess and intervene on the precision-weighting of prediction errors along the cognitive and emotional processing hierarchy and conclude by discussing the clinical relevance of interoceptive technologies in terms of diagnostic stress tests for evaluating interoceptive abilities across clinical conditions and as intervention protocols for conditions such as generalized anxiety disorders, post-traumatic stress disorders, and autism spectrum disorders.

Invasive Brain Computer Interface for Motor Restoration in Spinal Cord Injury: A Systematic Review.
Jordan J. Levett
Lior M. Elkaim
Farbod Niazi
Michael H. Weber
Christian Iorio-Morin
Alexander G. Weil
Investigation of the Dosimetry Characteristics of the GAFCHROMIC® EBT3 Film Response to Alpha Particle Irradiation
Mélodie Cyr
Victor D. Martinez
S. Devic
Nada Tomic
David F. Lewis
S. Enger
Lag-Llama: Towards Foundation Models for Probabilistic Time Series Forecasting
Kashif Rasul
Andrew Robert Williams
Marin Biloš
Hena Ghonia
Anderson Schneider
Sahil Garg
Yuriy Nevmyvaka
Over the past years, foundation models have caused a paradigm shift in machine learning due to their unprecedented capabilities for zero-sho… (see more)t and few-shot generalization. However, despite the success of foundation models in modalities such as natural language processing and computer vision, the development of foundation models for time series forecasting has lagged behind. We present Lag-Llama, a general-purpose foundation model for univariate probabilistic time series forecasting based on a decoder-only transformer architecture that uses lags as covariates. Lag-Llama is pretrained on a large corpus of diverse time series data from several domains, and demonstrates strong zero-shot generalization capabilities compared to a wide range of forecasting models on downstream datasets across domains. Moreover, when fine-tuned on relatively small fractions of such previously unseen datasets, Lag-Llama achieves state-of-the-art performance, outperforming prior deep learning approaches, emerging as the best general-purpose model on average. Lag-Llama serves as a strong contender to the current state-of-art in time series forecasting and paves the way for future advancements in foundation models tailored to time series data.
Mining Mass Spectra for Peptide Facts
S. Lemieux
The current mainstream software for peptide-centric tandem mass spectrometry data analysis can be categorized as either database-driven, whi… (see more)ch rely on a library of mass spectra to identify the peptide associated with novel query spectra, or de novo sequencing-based, which aim to find the entire peptide sequence by relying only on the query mass spectrum. While the first paradigm currently produces state-of-the-art results in peptide identification tasks, it does not inherently make use of information present in the query mass spectrum itself to refine identifications. Meanwhile, de novo approaches attempt to solve a complex problem in one go, without any search space constraints in the general case, leading to comparatively poor results. In this paper, we decompose the de novo problem into putatively easier subproblems, and we show that peptide identification rates of database-driven methods may be improved in terms of peptide identification rate by solving one such subsproblem without requiring a solution for the complete de novo task. We demonstrate this using a de novo peptide length prediction task as the chosen subproblem. As a first prototype, we show that a deep learning-based length prediction model increases peptide identification rates in the ProteomeTools dataset as part of an Pepid-based identification pipeline. Using the predicted information to better rank the candidates, we show that combining ideas from the two paradigms produces clear benefits in this setting. We propose that the next generation of peptide-centric tandem mass spectrometry identification methods should combine elements of these paradigms by mining facts “de novo; about the peptide represented in a spectrum, while simultaneously limiting the search space with a peptide candidates database.
Open design of a reproducible videogame controller for MRI and MEG
Yann Harel
André Cyr
Julie Boyle
Basile Pinsard
Jeremy Bernard
Marie-France Fourcade
Himanshu Aggarwal
Ana Fernanda Ponce
Bertrand Thirion
Pierre Bellec
Videogames are emerging as a promising experimental paradigm in neuroimaging. Acquiring gameplay in a scanner remains challenging due to the… (see more) lack of a scanner-compatible videogame controller that provides a similar experience to standard, commercial devices. In this paper, we introduce a videogame controller designed for use in the functional magnetic resonance imaging as well as magnetoencephalography. The controller is made exclusively of 3D-printed and commercially available parts. We evaluated the quality of our controller by comparing it to a non-MRI compatible controller that was kept outside the scanner. The comparison of response latencies showed reliable button press accuracies of adequate precision. Comparison of the subjects’ motion during fMRI recordings of various tasks showed that the use of our controller did not increase the amount of motion produced compared to a regular MR compatible button press box. Motion levels during an ecological videogame task were of moderate amplitude. In addition, we found that the controller only had marginal effect on temporal SNR in fMRI, as well as on covariance between sensors in MEG, as expected due to the use of non-magnetic building materials. Finally, the reproducibility of the controller was demonstrated by having team members who were not involved in the design build a reproduction using only the documentation. This new videogame controller opens new avenues for ecological tasks in fMRI, including challenging videogames and more generally tasks with complex responses. The detailed controller documentation and build instructions are released under an Open Source Hardware license to increase accessibility, and reproducibility and enable the neuroimaging research community to improve or modify the controller for future experiments.
OpenForest: a data catalog for machine learning in forest monitoring
Forests play a crucial role in Earth's system processes and provide a suite of social and economic ecosystem services, but are significantly… (see more) impacted by human activities, leading to a pronounced disruption of the equilibrium within ecosystems. Advancing forest monitoring worldwide offers advantages in mitigating human impacts and enhancing our comprehension of forest composition, alongside the effects of climate change. While statistical modeling has traditionally found applications in forest biology, recent strides in machine learning and computer vision have reached important milestones using remote sensing data, such as tree species identification, tree crown segmentation and forest biomass assessments. For this, the significance of open access data remains essential in enhancing such data-driven algorithms and methodologies. Here, we provide a comprehensive and extensive overview of 86 open access forest datasets across spatial scales, encompassing inventories, ground-based, aerial-based, satellite-based recordings, and country or world maps. These datasets are grouped in OpenForest, a dynamic catalogue open to contributions that strives to reference all available open access forest datasets. Moreover, in the context of these datasets, we aim to inspire research in machine learning applied to forest biology by establishing connections between contemporary topics, perspectives and challenges inherent in both domains. We hope to encourage collaborations among scientists, fostering the sharing and exploration of diverse datasets through the application of machine learning methods for large-scale forest monitoring. OpenForest is available at https://github.com/RolnickLab/OpenForest .
SAGE: Smart home Agent with Grounded Execution
Dmitriy Rivkin
Francois Hogan
Amal Feriani
Adam Sigal
Steve Liu
Spatial Distribution Modeling of Pistacia atlantica using Artificial Neural Network in Khohir National Park
Tymour Rostani Shahraji
Reza Akhavan
Reza Ebrahimi Atani
Tuning Minimum-Norm regularization parameters for optimal MEG connectivity estimation
Elisabetta Vallarino
Ana Sofia Hincapié
Richard M. Leahy
Annalisa Pascarella
Alberto Sorrentino
Sara Sommariva
The regularization parameter of the Minimum Norm Estimate of neural activity impacts connectivity estimationWe study empirically the optimal… (see more) parameter for connectivity estimation using realistic synthetic datasetsWe find the optimal parameter for connectivity estimation is systematically smaller than the optimal parameter for source imaging; different connectivity metrics yield the same resultCode and data are available open source.
Adaptive Resolution Residual Networks
We introduce Adaptive Resolution Residual Networks (ARRNs), a form of neural operator that enables the creation of networks for signal-based… (see more) tasks that can be rediscretized to suit any signal resolution. ARRNs are composed of a chain of Laplacian residuals that each contain ordinary layers, which do not need to be rediscretizable for the whole network to be rediscretizable. ARRNs have the property of requiring a lower number of Laplacian residuals for exact evaluation on lower-resolution signals, which greatly reduces computational cost. ARRNs also implement Laplacian dropout, which encourages networks to become robust to low-bandwidth signals. ARRNs can thus be trained once at high-resolution and then be rediscretized on the fly at a suitable resolution with great robustness.
Criticality of resting-state EEG predicts perturbational complexity and level of consciousness during anesthesia.
Charlotte Maschke
Jordan O'Byrne
Michele Angelo Colombo
Melanie Boly
Olivia Gosseries
Steven Laureys
Mario Rosanova
Stefanie Blain-Moraes
Consciousness has been proposed to be supported by electrophysiological patterns poised at criticality, a dynamical regime which exhibits ad… (see more)aptive computational properties, maximally complex patterns and divergent sensitivity to perturbation. Here, we investigated dynamical properties of the resting-state electroencephalogram of healthy subjects undergoing general anesthesia with propofol, xenon or ketamine. We then studied the relation of these dynamic properties with the perturbational complexity index (PCI), which has shown remarkably high sensitivity in detecting consciousness independent of behavior. All participants were unresponsive under anesthesia, while consciousness was retained only during ketamine anesthesia (in the form of vivid dreams)., enabling an experimental dissociation between unresponsiveness and unconsciousness. We estimated (i) avalanche criticality, (ii) chaoticity, and (iii) criticality-related measures, and found that states of unconsciousness were characterized by a distancing from both the edge of activity propagation and the edge of chaos. We were then able to predict individual subjects’ PCI (i.e., PCImax) with a mean absolute error below 7%. Our results establish a firm link between the PCI and criticality and provide further evidence for the role of criticality in the emergence of consciousness.